SMTL ID : 4d2c.1

Structure of a di peptide bound POT family peptide transporter

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

4 x 78M: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78M.1: 9 residues within 4Å: Chain A: R.85, P.86, F.89, W.90, Y.193, Y.194, G.197, K.198, L.206 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.89, A:F.89, A:F.89, A:W.90, A:Y.194 Hydrogen bonds: A:R.85, A:Y.193 78M.2: 8 residues within 4Å: Chain A: M.238, W.243, A.248, N.251, L.252, I.255, A.259, F.263 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.252, A:I.255, A:I.255, A:A.259, A:F.263 Hydrogen bonds: A:W.243 78M.4: 3 residues within 4Å: Chain A: A.376, L.377 Ligands: 78N.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.377 78M.5: 10 residues within 4Å: Chain A: Y.335, L.370, Y.378, V.384, S.385, L.387, W.388, G.391, A.394, L.395 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.370, A:L.370, A:L.387, A:L.387, A:W.388, A:A.394, A:L.395 Hydrogen bonds: A:S.385, A:S.385, A:W.388

2 x 78N: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE(Non-covalent)

78N.3: 6 residues within 4Å: Chain A: L.369, A.372, I.373, A.376, V.451 Ligands: 78M.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.369, A:L.369, A:A.372, A:I.373, A:I.373, A:A.376 Hydrogen bonds: A:A.376 78N.6: 6 residues within 4Å: Chain A: F.76, V.77, I.81, L.212, V.217, V.224 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.76, A:F.76, A:V.77, A:I.81, A:L.212, A:V.224 Water bridges: A:L.212

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: D.48, F.106, G.107, A.108, S.109 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.48, A:G.107, A:A.108, A:S.109, A:S.109, A:S.109, A:S.109

1 x ALA: ALANINE(Non-covalent)

ALA.8: 9 residues within 4Å: Chain A: Y.30, I.155, N.156, A.159, N.328, P.329, I.332, E.400 Ligands: PHE.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.159, A:P.329 Hydrogen bonds: A:N.328, A:N.328

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.9: 8 residues within 4Å: Chain A: R.26, Y.30, Y.68, K.126, I.155, W.427, S.431 Ligands: ALA.8 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.68 Hydrogen bonds: A:Y.30, A:Y.30, A:Y.30, F.9 Salt bridges: A:R.26, A:K.126 pi-Stacking: A:F.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyons, J.A. et al., Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters. Embo Rep. (2014)

Release Date

2014-06-25

Peptides

Di-or tripeptide:H+ symporter: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Di-or tripeptide:H+ symporter

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